Dark Child the Return
by Midnight Lost
Summary: Episode 3 is now up and has been reedited. The final conclusion of the Dark Child the Return trilogy! ShinjixRei pairing.
1. Episode 1

-1Dark Child: The Return

Episode 1: Assimilation

By: shinjitheassassin

Original Story Concept by: Gunman 

Authors Notes: I would like to start off by saying this is only a side fic, an alternate outcome to Gunman's Dark Child series taking place roughly a three years after the third chapter. The events in this fic do not follow the storyline the original author has intended. This is more of an alternate universe. I hope everyone enjoys this as I try to keep it as close to its original concept.

**!WARNING!**

This story contains a lime/lemon scene, that contains material not suitable for younger readers. Parental guidance is advised. If you are under the age of 18, do not read any further. Remember the ceiling cat is watching YOU!

(Nerv Headquarters)

"Commander Ikari is dead. Both Shinji and Rei are gone. Considering this, I think it's time you all knew the truth." Fuyutsuki said.

"Truth? What truth?" Misato asked, as the word 'truth' caught Kaji's ear.

"The truth about the Angels, and why NERV really exists." Ritsuko stated.

"That would not be a good idea." a familiar voice stated. Catching the attention of everyone in the room to look to the door where the newcomer was. Stepping into the little light the room had to offer, everyone gasped in surprise. Though they had just seen him killed, Gendo stood in the door way.

_Just like the bastard to clone himself _Ritsuko thought to herself.

"C-c-commander?! But I thought….."Maya stammered, dumbstruck by the sudden appearance of the one they had just seen killed moments ago. "But how?"

"That is irrelevant." The commander stated walking over where his previous self was and removed a small item from the pocket which had just barely missed from being cut. Turning his attention to his second in command. "Report on what has just happened in five minutes" he said and turned, walking out. "And clean up that mess."

"That was…. Weird." Asuka said as she stared on, her eyes darting back and forth between the mess that once was the commander, then to the commander who had walked out the door. The rest just remained there speechless. It took minutes for everyone to regain their composure, a Nerv detail crew had already reported to remove what was left of the former commander, carting him out in eight body bags. Fuyutsuki had left to go report the matter to the new commander.

(Commanders Office…I guess you would call it)

"I said in five minutes." Gendo cut to the chase, his second in command was nearly a minute late.

"I apologize, I was getting the video feed that had recorded the incident." the elderly man stated as he handed the commander a disc. "I figured it would be easier then trying to explain it with words."

"Indeed." the commander stated, and placed the disc he had just received into the terminal on his desk. Viewing the event. Though he couldn't be seen behind his gloved hands that once again sat bridged before his mouth, he made a frown in disgust. "Where are they now?"

"We don't know sir, they seemed to have just disappeared."

"I see." the commander replied. "Order all security personal to shoot the third child on sight, I will not have this incident repeated. Also, continue the search for the First Child."

"Yes sir." the elderly man answered, and left to do so.

However many thoughts bothered Gendo, though his face did not betray it. _This is going to prove a problem in our project, I cant simply revive a new Rei without the others becoming more curious then they already need to be._ He then took out the small item he had taken from his former self and reset it. It was a heart sensor, so that if the persons heart stopped beating, a new Gendo would awake, however there was no need for it anymore, he was the last one.

(Above Ordo 7)

Blaster fire surrounded The Infiltrator as Shinji maneuvered it to avoid the firestorm that besieged them. Rei was in the co-pilot seat focusing on keeping their rear deflector shields up as another barrage hit them. They had failed to assassinate Sidious and were forced to flee; their allies dead. Shinji had moved to soon to claim revenge for his former master and with his confidence in his power and team he had foolishly under estimated the Sith Lord. The Infiltrator was a fast and maneuverable ship, capable of out running most of the fleet easily, but the ship that now pursued them was The Chikara, a prototype battle cruiser. Despite its large bulk it was able to keep up with them. It had the appearance of an over sized blimp, Shinji couldn't help think. (A/N: Think Protoss Carrier from Starcraft would best fit the description) It released another squadron of TIE fighters to attack the Naboo ship. Then the large blimp did something that surprised Shinji, stopping its pursuit, the ship then began to split into quarters, long ways down its haul.

"MASSIVE ENERGY READING EMITTING FROM THE SHIP!" Rei exclaimed.

A green glow came from the parted ship as it continued to build up energy to fire its primary, and secret weapon. This weapon was the prototype of what would later be on the Death Star.

"Its locked on to us" she continued, a hint of worry in her voice.

"Do not worry, such a beam no doubt will take time to recharge." Shinji calmly said as he used the Force to navigate his way through the laser blasts that continued to fall upon them from the TIE fighters. "I have an idea."

"If that things hits us, its over."

"This is true, however a weapon of that energy will require a large amount of power and will no doubt keep it from moving forward when its fired, if it misses it will give us the time we need to make our escape" Shinji explained.

"I trust you." Rei replied. Time seemed to have stood still as she looked over at the man in the pilot seat, in the time she had stood by his side, so much has changed. With their training, and missions. Those who had once known the two would hardly recognize them now. She then couldn't help but wonder how their former comrades would see them now. She was soon shaken out of her thoughts as a bright green light shot passed them as Shinji just barely maneuvered the ship, his timing just right. The beam passed The Infiltrator and hit the planet below them, just happening to hit exactly where the temple was that originally took Shinji back to his home. The next series of even happened in the blink of an eye. Within seconds after the beam hit the planet, the planet began to crack, a jade green light pushing through the cracks as the planet began to break apart. Then it erupted into a massive explosion, the jade light flowing out, engulfing both ships before retracting back into itself, pulling both The Infiltrator and The Chikara with it, disappearing; one of the TIE fights managed to get one last shot off, hitting The Infiltrator, disabling their main power drive before being crushed by the force of the explosion.

(Earth; Our Dimension)

"Report on the progress of your search for the First Child." Gendo stated, looking at his second in command.

"Nothing yet sir." the elderly man answered.

"I see, she must be found." the commander said. _'Our future depends on it'_

It had been two weeks since Rei had disappeared from the command center. Most of the staff was on edge, especially those who were present during the incident, though no one wanted to talk about it. Misato was on the verge of a mental break down at the loss of Shinji, the apartment had quickly fallen apart. Asuka on the other hand had been glowing with praise, as she was the only remaining Eva pilot, pushing her stock through the roof. However there was a problem in this, since the disappearance of Rei, the Angels had ceased their attacks, proving frustrating to the Second Child. Though no one could tell why, but assumed it was only a matter of time before they would attack again. Ritsuko had locked herself in her office most of the time, doing who knows what.

Meanwhile, above the earth a brilliant green light flashed, spitting out The Infiltrator, spinning it wildly as the occupants struggled to regain control as the ship plummeted towards the planet. Using its many thrusters to straighten out the ships course.

"Fire the emergency booster engines!" Shinji ordered. Rei did so, the ship began leveling out allowing them to regain control.

"Secondary power at fifty percent, we're going to need to land for repairs." Rei stated as she over looked her console, alarms sounding throughout the ship. It was then that Shinji noticed the planet they were heading to, though they still couldn't see anything that would serve as a marker to where they were, there was a strange sense of familiarity to it. It then occurred to Shinji where they were, a smile crept across his face.

"Rei?"

"Yes Master?"

"Does anything look familiar?" he asked

Rei took a moment to observe out the window in front of her, she couldn't recall anything. Then it hit her, this was….home. She smiled, soon her previous thoughts would become a reality, what would her former comrades think of her now. Shinji continued to pilot, choosing to land the silver ship a few miles outside of Tokyo-3 in the dense forest, this would offer natural cover for them to go unnoticed. He wanted to land as quickly as possible, not know when or if their pursuers would attack again. Setting down in an ideal spot, surrounded by trees large enough to conceal the silver ship. Shinji swiveled his chair around, punching random buttons on the monitors, running a complete systems check to get the full report on everything that was damaged. They were lucky, the damage was minimal, something they could fix easily.

"Small breach in the power core, and minimal system damage to the shields."

"Can we fix it?"

"Yes, we have enough supplies on board to do so." he replied. "It will take some time though."

"I understand." Rei said and left the cabin, setting off to begin the repairs. During her adventures with her husband she had learned the mechanics of the ship rather well, mostly due to trial and error, though he had been there to guide her. Shinji had followed after her. The two spent nearly half the day doing repairs, and making little headway as complications ensued, or rather distractions as they worked close together. In the fading light, they decided to set up camp. Digging into their survival units for their meals. Seeing the weather was nice they decided to eat outside, starting a small camp fire. Despite all the technology they had, years beyond anything currently on earth, this seemed more comfortable. Silence hung over the two as they ate, until Shinji spoke up.

"I feel I must apologize." he began, remnants of his former self partly showing.

"What for?" Rei asked, confused.

"I forced you to come with me, when I came back." he explained. "I drugged you to make you mine."

Rei smiled. "Mind tricks only work on the weak minded." she simply replied.

"What do you mean?"

"I would have come for the asking." she revealed. Though the pill had done its job, she allowed herself to fall under his influence that day. The truth was, she wanted to go with him, she wanted to be rescued from that life; she wanted to be desired and needed. Shinji smiled as he looked at her.

"Rei-chan?"

"Yes?"

"Do you love me?"

"Yes Shinji-kun."

"Will you promise to serve me, as my lover and partner? As my bride?" he asked, moving closer to her, staring into her crimson eyes as he spoke these words.

"Yes, my lord." she smiled, pulling him closer to her as she answered. Their lips meeting passionately. Laying back she pulled him on top of her, continuing to kiss each other. Shinji then broke the kiss.

"Then I take you as my bride, Rei Ayanami. You will love me and no other. You will desire no other but me."

"Yes, my love."

"You are mine forever, Rei-chan. Because I want to love no one else." he said as he looked into her crimson eyes as he embraced her for another kiss, which she returned with the same force and passion. The pledge reset and cast in stone.

He brought his right hand, placing it at the small of her back to support her as she grasped the back of his neck, keeping him close to her as they continued to kiss, heat building between the two. Slowly they began to strip each other of their Sith garments. Exposing her breasts, he began to kiss down her neck, slowly, teasing her as he went, gasps escaping her lips as he proceeded. Reaching her firm breasts, he took one in his mouth, gently sucking on its nipple, while his hand cupped the other, pinching its nipple between his finger and his thumb. Electricity was coursing through her body as waves of pleasure washed over her again and again. As his mouth continued to keep one of her breast occupied, he finished removing the rest of her lower clothing, leaving her completely exposed to him. Stopping for a moment he looked up at her, her eyes were closed. Smiling he leaned down again, kissing her deeply on the lips before leaving a trail of kisses and soft bites down her body, licking the valley between her breasts and continued kissing along her sensitive stomach. He then reached her lower regions, She let out a surprised gasp as he probed her entrance with his tongue, spreading her lips apart with his fingers, he continued to work her vessel, probing his tongue in and out, and flickering it along her clit. Moans followed forth from her lips, arching her back, she cried out as she came, unable to control it any longer. That finished, Shinji smiled and began working his way back up her body, reaching her lips again. Pressing his lips against her, they began another passionate kiss, their tongues snaking around each other. She spread her legs more, to offer him entrance. His hardened member rubbing against her entrance, causing her to gasp in anticipation. Slowly he pushed himself in, slowly working his way until he was at the hilt. Settling there for a moment, he began to thrust himself in and out. Deeply kissing her as moans escaped both of them, moans of pleasure, unbridled pleasure. They continued for hours, altering positions as they went. Not stopping until well into the late evening, before Shinji finally came, releasing his essence and planting it deep within her body. Finally the two succumbed to sleep, pulling the sleeping bag up around them, snuggling close together, giving one another one last kiss good night.

(NERV, earlier that day)

Typing could be heard throughout the dark corridor to anyone who would chance to be down in the lower depths of Central Dogma. The light from the small computers monitor reflecting off the unshaved mans eyes.

"So. that's what it is." he spoke softly to himself. Since the sudden return of the commander he had become curious to the events. He had seen the commander killed, only to have a new one appear. After two weeks of hacking and digging he had finally uncovered the truth behind it. "Seems he's not a very popular guy." he smirked. There was a sudden crash just down the corridor, quickly he shut off the computers monitor and pulled out his side arm, sitting silently waiting to see what it was. He then felt something press against the back of his head.

"Find what your looking for?" a familiar voice said.

Lowering his gun he replied. "Feeling better?"

"Yes, thank you for your concern." Misato said, a hint of venom in her voice. "Now why are you down here?"

"Well you see, I was curious." he began, in his usual swagger.

"Of what?"

"Our commander, we saw him sliced into eight pieces, thrown against the wall; and yet he is alive."

"So he had a body double, not uncommon."

"Yes that was what I first thought too, but I was satisfied with just that. So I did a little digging, and guess what I found." he smiled as he reopened his lap top revealing medical documents for Ikari, Gendo. Misato looked in shock.

"Complete genetic replication, he was a…..clone?"

"Is a clone, turns out the original Gendo Ikari died shortly after second impact, these copies have been continuing his work."

Misato was at a loss for words as this was revealed to her. But then again, it slowly crept into her mind that it made sense, he was always detached from everyone else. Lowering her gun from his head, securing it back in her holster.

"Also, I pulled up the video feed from the other day."

"What video?" she was still confused at first but it came back to her. "Oh, did you find anything new?"

"Well not really, but I found an answer to every ones questions."

"Was it Shinji?"

Kaji quickly punched a few of the keys, opening a new file on the computer. Playing the video in questions, then slowing it down very slowly as the camera that was in the room zoomed in for a close up shot as the man looked at the blue haired pilot. "Here you can see his expression soften, a very familiar face."

"IT IS SHINJI!" Misato exclaimed, then quickly slapping her hand over her mouth, remembering where they were. "But how did he change? And get so big?"

"That I can not answer, the only thing I know is that it was him. I am also curious as to how he returned and why he only took the First Child with him."

The two froze as they heard another pair of footsteps down the main corridor. Kaji quickly shut his monitor and pressed himself and Misato against the wall to reduce the chances of being seen. Two figures passed, one of a woman, the other a man.

"Are you sure about this sir?" the woman asked.

"There is no other way, we need the first child to proceed." he replied as the two entered a large room surrounded by an aquarium like tank. The woman walked over to an instrument panel and read the results, satisfied she turned to the man.

"When do we begin?"

"We will begin in two days, giving the third time to heal." the man replied.

"Wont the sudden appearance of the first child bring about unneeded attention from the others?"

"No need to worry, we will simply report that we had located her."

"I see."

"Let us go, we have much to do."

"Yes sir."

With that the pair left, not once noticing that they have been overheard. The foot steps faded away, as a mechanical hum signaled that they had entered the elevator.

"And so another piece of the puzzle falls in our laps." Kaji smiled.

(The Infiltrator)

Morning found the two Sith cuddled close together, their fire had gone out sometime in the early morning hours. Shinji slowly stirred awake, smiling as he saw the azure haired girl laying in front of him, her crimson eyes looking up into his.

"Morning Rei-chan" he smiled, kissing her forehead gently.

"Morning Shinji-kun" she beamed. The two of them got up from where they laid and proceeded to secure their attire. Donning their usual all black clothing. Shinji thought for a moment as he looked at Rei. She noticed and smile.

"What are you thinking about?"

"I feel I need to give you a proper name" he replied.

"Proper name?"

"A Sith name" he paused for a moment, then smiled. "Rei Ayanami, from this day forth, you shall be known as Darth……Shi"

"Shi? Death." Rei stated.

"Yes, fitting for one who accompanies a demon."

This brought a smile to the blue haired woman, kneeling down before him she bowed her head. "Thank you, my master"

"Arise, Darth Shi, I have an assignment for you."

"What is it, my master?"

Shinji smirked. "I want you to return to Nerv, and negotiate its complete surrender to me by any means necessary." he stated, though it had seemed like a lifetime ago, he recalled the military organization he once served by force. Returning now, he saw the advantages he would have having such a group under his command.

"It will be done my lord"

"Go now, I will arrive there within a day, after I complete the final repairs" he said. With that, Rei secured her own light saber to her belt and set off in the direction of the city, wrapping her black cloak about her, placing its hood over her head. Taking one last look behind her, she didn't want to leave him, but he had given her a mission to do on her own, and she would not fail him. Turning, she left, leaving the wooded area. Tokyo 3 was no more then two miles away, a distance she covered easily as she walked on, gaining curious stares from some of the people along the streets as she made her way through its down town area. She didn't pay no mind to them as she continued on her way. After two hours of walking, she reached her destination, standing in front of a line of doors that led into the Nerv base. Looking down she saw the card slot for employees and others to slide their card through to gain entrance. She frowned some at this, she had lost her ID card years ago, her frown then became a grin, raising her hand she moved it sideways, causing the doors to open as she extended out with the Force. She then entered, she was immediately stopped by two guards. Rei smirked as she looked at the two guards, brining up one hand she extended two fingers towards the first, for some reason causing him to convulse against the wall, then turned to the second, doing the same. She then moved on leaving both guards to die as they gasped their final breathes. Continuing on she rounded her second corridor, she had been in the building enough times before to know where she was going. She was then stopped when someone called her name.

"Rei?" a female voice asked from behind her. Before she had time to answer the woman behind her hugged her, almost tackling her. "REI IT IS YOU!" Misato exclaimed. Rei did not take kindly to this physical action, but gathered nearly every ounce of will power in her body not to cut the purple haired womans head off. "Commander Ikari is going to be pleased to see you were able to escape!"

Rei did not comment at first, turning around to face the major behind her. "I must speak with commander Ikari at once, its very urgent I do so." She repeated

"Of course, I will let him know right away, in the meantime lets get you changed into something more comfortable."

"These are fine, please the commander." Rei was becoming impatient to say the least, and it was starting to sound in her voice. Misato nodded in acceptance andled Rei down the series of corridors that made up the Nerv complex. They soon arrived at two large black doors. Two more guards where posted there. Due to the incident Ikari had stepped the security up, everyone had to be searched before entering his office. While one guard stood ready at the door, gun in hand, the other proceeded to remove Misatos gun, the moved to Rei, patting her down, finding her light saber; though he didn't know what it was. Again Rei didn't like it but held back as the guard led the two into the room where Gendo sat behind his desk, his hands folded across his mouth. The guard set the two weapons on the desk before him and quickly turned to leave, not saying a word.

"What is it Major?" Ikari asked as he looked over the two, his eyes focusing on Rei for a moment.

"Sir, Rei Ayanami has returned."

"Where is she?"

Misato said nothing at first as she gestured to the eighteen year old woman beside her. "This is Rei Ayanami."

"I see" the commander answered as he studied the girl in front of him. Noting the eerie resemblance of the clothing to that of his former selfs attacker.

"Sir;" Rei began, "I request that Dr. Akagi and the remaining Eva pilot accompany us here to hear what I am about to say, for it surely will affect them as well as the rest of Nerv." the names coming to her mind as she continued.

Gendo frowned at this but nodded, pressing the intercom button on his desk. "Bring Dr. Akagi and the Second Child to my office." he said, canceling the communication before he got an answer.

"Can I get you anything to drink Rei?" Misato asked, becoming more cheerful like her usual self.

Rei frowned for a second, they wouldn't have any of the drinks she enjoyed at the cantinas, she then looked at Misato.

"Tea would be fine" she answered, it was all the really had to offer. Misato nodded and left. Returning a few minutes later with a paper cup from the vending machine in the break room. Rei accepted it, but offered no thanks. Soon the other two arrived.

"WONDER GIRL!" Asuka cried out when she saw the blue haired woman. If looks could kill, Asuka would have been dead from the glare she had received from Rei, causing the red head to flinch under her eyes. She had always hated being called that, and if she wasn't careful, Asuka would be called 'Dead Girl' Rei thought to herself.

"You said you had information pertaining to the future of Nerv, what is it?" Ikari stated from his chair, getting straight to the topic at hand.

"Of course" Rei looked to him, a slight smile flashed on her face. "I have vital information about the attacker." she began.

"And that is?"

"He is planning an attack on this base." she simply stated. "He will assume control of it" she continued , her tone of voice absolute.

The commander frowned again. "And how does one man take over an entire base? It is of no concern, he wont make it passed the front gates." Ikari counted, fully confident in his security. "But I am curious Rei, tell us your story, what happened after he kidnapped you?"

Rei smiled again as memories flashed in her mind, but the smile was brief as she looked over the commander. "Very well, I will tell my story to you." She then proceeded to recount the events that took place after her 'abduction'. She left out their marriage, not wanting to draw any suspicion to herself and about how he had taken her on as his apprentice, this was more to explain the clothing she was wearing, having seen the worried look upon the commanders face. When she had finished she took another drink of her tea, which had cooled off.

"I see."

"But how did you escape from him?" Misato asked. This time Rei smiled, large enough for everyone to see. This no doubt brought about fear in them.

"Escape? Who said I escaped." Rei grinned.

"But you…."

"I said nothing of the sort, you assumed" Rei pointed out. During this time Gendo had paged the two guards to enter the room. Rei smirked again. _This is going to be fun_ she thought as she glanced behind her. "Don't trust me Commander?" she asked, mocking the innocence in her voice.

"There is nothing you can do Rei, with your weapon right here." Gendo stated as he patted the light saber next to him on the desk. He had reviewed the video enough to know that what it was, though he didn't know its name.

Rei smiled again "I no longer go by the name Rei Ayanami." she stated. "My name is Darth Shi." a hint of hatred and anger in her voice. At this the two guards behind her raised the guns, aiming at her back, ready to open fire. The next few actions happened fast. Without so much as a warning Rei reached out her right hand towards the desk, stretching out with the Force and grabbing her light saber, brining it to her hand as she jumped up. Igniting it as she spun around in the air, she landed behind the guards before they had a chance to turn around, she slashed across them, cutting them in half at their waist. She then turned around, facing the door and threw out her left hand, slamming the doors shut before the others could escape. Grinning she turned to face the horrified Commander. Extinguishing her saber she raised her left hand and made a movement of pinching something in mid air between her two fingers and thumb. As she did this, Ikaris hands came up to his throat as he tried to breath, something was choking him.

"Now that I have your attention Commander, I will give you one chance that might save your life. Surrender all of Nerv to my Master." she stated coldly.

_Master? _Asuka thought to herself as she stared on in horror. Even greater fear gripped her when she realized she might be next due to the fact that constantly in the passed she had always bullied Rei

"I…..I-I ca-n't" Ikari struggled to speak. At this Rei released him from her grip and sighed.

"I see, well I supposed we will do things the easy way." she smirked again, leaping forward landing on top of the desk, igniting her saber again, swung at a slant. For a few seconds Gendo sat their, a shocked look at his face. Then a line began to form running from the top right of his head towards his left cheek, as the top part slid down, landing on the floor, leaving the body remaining in the seat with half a head.

"Its finished, all of Nerv is under my command until my Master gets here." Rei stated as she extinguished her saber, securing it back on her belt. Pushing the body out of the seat she sat down in it, not even second glancing the corpse.

"He's….. he's coming here?" Asuka asked in fear.

"Yes, he will arrive shortly, and I warn you, he is not as forgiving as I am." she warned. "Have someone clean up this mess." with that she dismissed the remaining three in front of her. She then turned her attention to the elderly man who lay on the floor just behind her, gasping for breath. The events that had transpired had triggered a severe heart attack. Smirking some she looked around the dark room, the sepheroth tree painted on the ceiling above her. Within hours a report came to her desk stating that an unidentified object was approaching their location. With that news she ordered all personal to the inner landing pad just inside the Geofront. The soilders standing at attention as the silver ship descended, two separate groups of them, creating a path down the center where the ship landed, lowering its boarding ramp. Rei approached the entrance and kneeled down, bowing her head as another cloaked figure descended the ramp.

"Arise Darth Shi." the man said. She did so

"It is done my lord."

"Good, very good. Everything is going according to plan" he smiled as he turned to look at her while the walked.

"Yes, the beginning of your own empire" Rei coolly remarked with a grin.

"_Our _empire." he corrected her. "Every emperor needs and empress." he smiled.

To Be Continued…..

Authors Notes: Well there it is, Part 1 of the Dark Child side fic series, At this time I am not sure how many parts there will be. I would like to thank Gunman for giving me permission to do this side fic, and hope that I have stayed true to its original concept. As stated previously this is an alternate universe fic as to what would happen if Shinji and Rei returned and took over Nerv and so on. There are some references to the original Star Wars movies, like Rei force choking Gendo. I hope everyone enjoyed reading it as much as I did writing it. Also there are a few other Japanese words in this:

Chikara Power

Shi Death

Oni Demon

For those who are curious, Reis light saber is much like Darth Mauls, except it can be split into two separate sabers.

Pre-Readers

Gunman

My room mate, always hanging over my shoulder

Special Thank to Gunman for allowing me to run with this.

Disclaimer: I do not own Evangelion or any of the Star Wars characters, those are property of their respected owners. Evangelion belonging to Gainax and its respected affiliates and Star Wars to George Lucus.


	2. Episode 2

Dark Child the Return

Episode 2: Dark Force Rising

By: shinjitheassassin

Original Story Concept by: Gunman

Authors Notes: I would like to thank everyone for their comments, reviews and suggestions from the previous chapter. So we got Shinji and Rei now in control of Nerv, but yes how will Seele deal with this? Guess we will soon find out. Also this chapter is going to give everyone an idea as to what became of the Chikara and her crew. Enjoy.

Chikara Crash Site

An aging man stood atop of the sand dune dressed in a simple brown robe, looking out to the sea he had just come from. Waves of water washing over the sanded beach. His long grey hair blowing in the ocean breeze. A golden medallion hung about his neck, which his long grey beard nearly covered. His deep blue eyes gazed at the remaining soldiers that emerged from the water, he let out a soft sigh as he began recalling the details that had led them here.

Just before they were sucked into the warp they had accelerated to full power to close the gap between themselves and the silver ship that they were pursuing. This turned out to be their downfall as they came out of the time warp, only to be lost in the blue planets gravity, unable to level out as the ship descended towards the planet. The outer haul began to melt from the heat from entering the planets atmosphere, rendering most of its flaps unusable. Tossed around violently within the ship made it impossible to scramble to the escape pods. One had succeeded in doing so but was only rewarded when it got smashed by the tail end of the Chikara after being deployed. The old man had remained calm during this, keeping his wits about him as he shouted out orders to the crew on the bridge. Breaking through the atmosphere the large ship increased its speed, heading towards the large body of water just east of a large island. He caught a glimpse of the silver ship they were pursuing , their query had regained control of their ship and were making a landing somewhere on the island. The ship then lurched again to the right, the body of water rushing closer. There was a deafening sound as the ship splashed down into the water, a majority of its large haul buckling under the sudden impact. Water rushed into the ships openings, flooding most of the inside. Sparks flew out of the computer consoles as the water flooded into them, pushing everyone the bridge back against the far wall. After a handful of seconds went by the entire bridge was submerged. The occupants began their struggle to escape the water, having waited till the ship was full, the grey haired man pressed a small button on the console before its power finally gave out, blowing the doors off to allow them to escape. He then proceeded to lead the men out, twisting down the many corridors before finally escaping the ship through a hole that was formed from the crash. They finally reached the surface and swam towards land. Reaching land he stood up and made his way to a large sand dune that stood above the beach. Standing on top of it he turned and surveyed the men coming out of the water.

"Master C'baoth sir" a man in a grey uniform approached him.

"Yes Lieutenant, report"

"Sir, the ship is non salvageable" he began. "We have gathered as many of the supplies…"

"What of the crew?" the grey haired man cut him off, peering down at the man with his ice blue eyes.

"Only fifteen percent of the crew survived." the man answered.

"And of my apprentice?"

There was a brief pause before the man answered again. "Unknown sir, he was in the hanger bay at the time of the crash. With the condition the ship is in I fear it is unlikely that he survived."

C'baoth stared out at the sea once more, glaring at it for a moment before responding. "I see, gather the survivors and set up camp here tonight. We still have a fugitive to hunt down. Get some rest, we will start off tomorrow morning."

Nerv

It had been two weeks since Shinji and Rei had returned to Nerv and had assumed control over the base. Only meeting some resistance from a few employees, which were quickly put down, invoking even more fear among the rest. This only incited a small problem, those killed needed to be replaced. Looking over the paper in front of him that held the personals names that were killed. A computer tech, and two guards. Shinji frowned at this, he needed to find people to replace the three, but he needed to find those who would be easier to control. Getting up from the desk he turned and walked towards the window and peered out over the Geofront. A smile spread across his face, he had an idea.

"Is something wrong Master?" Rei had entered the room, and was standing behind him.

"We need to replenish those who were punished." he replied.

"Where will we acquire people with the skills required."

"Two of the positions are easy enough, and I have an idea for the third." he paused from a moment. "Call in Pilot Soryu."

Rei nodded and turned to leave. She knew where to find the second child, where she always was. Reaching the elevator she made her way towards the Eva cages. Sure enough the red headed girl was standing on the catwalk in front of the red, four eyed Eva, though there really hadn't been much use for it, the Angels that once plagued the base hadn't appeared in weeks. She turned as she saw Rei approaching her.

"What do you want Wond-" she broke off in mid sentence, still breaking herself of the habit of insulting the two, less she would end up like those who had resisted. This thought didn't appeal to her very well.

"I will allow that to pass this time." Rei grinned. This only served to frighten Asuka even more, her grin was very unsettling. "The commander wishes to see you, immediately"

"Yes Ma'am" Asuka half snapped to attention and took off running down the catwalk. Rei smiled after her. _'So amusing to manipulate her'_

Asuka wasted no time getting to the commanders room. As much as she didn't like following orders from the two, she was left with no other choice, either follow them or be killed. Stopping a moment outside the doors she took the time to catch her breath before pushing the doors open, walking into the room.

"You wished to see me sir?"

"Yes, I have a task for you to perform." he began.

'_Why cant wonder girl do it?'_ she thought to herself but was quickly brought out of her thought at his next words.

"If you succeed there may be a promotion for you." he smirked, though she couldn't see it in the shadows. "How would Lieutenant Soryu sound?" He knew the best way to seduce her fully under his command was to offer her power.

"What is it you wish me to do?" Asuka found herself asking, intrigued at the thought of being promoted.

"It is a simple task, tomorrow I wish for you to go to school and bring three people back here with you."

"Which three?"

"Your friend Horaki, Aida, and Suzahara." Shinji stated as he sat down behind the large desk. "That is all. You may go."

Asuka stood there for a second before turning to leave. Passing Akagi as she exited the room. Lost in her thoughts as she began to daydream to possibilities. She then realized that she could possibly out rank Misato if she continued, a sly smirk crept across her face. _"Perhaps working under these two wont be so bad after all'_

"Sir, you wished to see me?" Akagi asked as she stood in front of the commanders desk.

"Yes, I have a little project for you and your team….. If you think you are up to it."

"Of course we are sir!"

"Good" Shinji then produced a blaster he had brought from the Infiltrator. "I want you to examine this and replicate its technology." he explained as he used his Force powers to levitate the weapon to her. Grabbing it Ritsuko looked over it and nodded.

"It will be done sir." she smiled. Excited about being given the opportunity to tinker with newer technology.

"You are dismissed." With that Akagi turned and left the room, still looking over the blaster as she walked down the halls, towards her office where her crew team awaited her return for a report of what the commanders new project for them was. Needless to say they were all shocked when she informed them of their new project, though at the same time excited. Without further delays the team had set to work, first test was to fire the weapon to see how it should function, though they had not anticipated its power and had to treat a guard on the other side of the wall who was shot in the leg.

"It appears we are going to have to apply that paint we used for Unit 00s shield during the 5th angel attack for these walls." Maya commented as a couple of men took the injured guard to the infirmary.

Rei reentered the commanders room, seeing him staring out the window she gave a soft smile and walked over and stood beside him. Her crimson eyes peering out over the Geofront. The sight before her reminded her very much of some of the planets she had visited. "How are things progressing?"

"Everything is going according to plan." Shinji answered. "Though we still have on loose end to tie up."

"And what would that be Master?"

Shinji didn't answer right away, taking in a deep breathe he replied "Seele, no doubt they will move against us once they have discovered our plans for this base."

The Next Day

"Hey Asuka, where have you been. You've been absent for two weeks now." Hikari greeted her friend, worried about the sudden absence. "So have Ayanami and Ikari"

Asuka tensed up a little at Ayanamis name before turning to answer the class rep. "I don't think they will be returning to school. They have a lot to do at Nerv." she said, and it was true.

"Oh.. I see. So why have you been absent?"

"I've had to take care of things at Nerv as well, the last two weeks the base had under gone many changes." she explained, once again telling the truth. "Um where are the two stooges?"

"They ran to the school store, geez Toji is like a walking stomach, but why are you asking about them?" Hikari asked curiously.

Asuka sighed a little, she really didn't want to talk to the two but it was an order and her promotion was at stake. "I need to talk to them after class, if you would please tell them. I will also need to speak to you as well." she answered.

Hikari was a little worried about this, not liking the sound in Asukas voice. "Um….ok"

The rest of the school day went on as normal, for the most part. Kensuke was surprised that Asuka had wanted to talk to them, Toji for the most part was dreading the encounter, nothing good ever came from talking to Asuka. Hikari was worried, her friend sounded serious about needing to talk to the three of them, like it was important but she didn't want to do it. The final bell rang signaling the end of school, students started to clear the room, leaving only 4 still sitting at their desks. With a heavy sigh Asuka got up and looked to the other three, who were sitting in close proximity of each other.

'_Best way to do it is to just cut to the chase'_ Asuka reminded herself "The commander ordered that I escort the three of you to Nerv to see him." she informed the three. Kensuke got excited being able to actually see the inside of the Nerv base. Toji let out a groan in despair as Hikari just looked on in shock. "Its best not to keep the Commander waiting." Asuka suggested as she walked to the door. Kensuke was the first out of his seat as the other two followed reluctantly. They didn't talk much on the way, Asuka was too busy daydreaming about the possibly promotions she would be able to gain. Soon they reached the series of doors that allowed entrance to the base. Asuka swiped her card and gestured for them to go before her. Once they were inside, Asuka led them towards the commanders office, having to stop a few times to grab Aida by his ear to led him away from various rooms. Finally they reached the commanders office, bracing herself Asuka pushed the two larges doors open and led the three into the dark room.

"Sir, I have brought the three you have requested." Asuka announced to the man sitting behind the desk.

"Very good….. Lieutenant Soryu." he smiled. This brought delight to the redhead. "You are dismissed."

"Yes sir." With that Asuka left glowing with pride. Kensuke stood in awe that she had just gotten promoted. Toji noticed something familiar about the voice coming from the man as did Hikari.

"Yo Shinji, where've ya been?" Toji exclaimed as he began to make his way towards the desk, but stopped when he heard a hiss come from beside him followed by a low hum. The sound itself wasn't what stopped him but rather the warmth near his neck coming from the red glow just below his chin.

"That is close enough." a voice said from the left of him. He glanced over to see a blue haired, crimson eyed woman holding the saber.

"That is enough Rei." Shinji spoke as he stood up from his chair, waking around the desk to greet his newcomers. The three found it rather odd and unsettling at Shinji's new wardrobe, accustomed to seeing him wearing his usual dress shirt and slacks. This new outfit was different, far more darker. He didn't wear his cloak but still had his loose pants, black boots and a leather like vest that went passed his waist, two cylinder shaped items hung on both sides of him. Rei was dressed in a similar fashion.

"Yes Master." she responded and extinguished her saber, securing it back to her waist, before she moved over to Shinjis side. This bothered Hikari. _'I've never known Rei to be that aggressive to anyone. What happened to make these two change this much? And when did she start referring to Ikari as master?'_

"I would like to thank the three of you for coming on short notice." Shinji began. "Why did I bring you here you ask? Very simple; I have three job openings that I would like you three to fill." Kensuke's eyes lit up at these words.

"YOU MEAN I GET TO BE AN EVA PILOT?" Aida exclaimed.

"No" Shinji answered, "However with your computer knowledge I would like to put you with the MAGI group, to help support the base operations." he continued. As expected Kensuke jumped at the opportunity, leaving only Hikari and Toji. Reaching over the desk his called in Misato. Once she got there she asked her to escort Aida to the MAGI to begin his training, then turned to the remaining two.

"Um… What happened to your father?" Hikari asked

Shinji smiled some "He had to retire his command." he answered. There was something in the voice she didn't like, something dark. "Now, I have openings in two guard positions." He paused for a second seeing Toji about to object and turned to him. "If you work for me, I can get your sister into Nervs own hospital wing to expedite her recovery" he smiled, seeing Tojis resolve fading, he then lowered his head and nodded.

"I will take the position…. But only if my sister is taken care of." Toji announced, sighing in defeat. Hikari tensed up as Shinji looked at her.

"Of course" Shinji answered.

"Now, you have shown good leadership skill while in the class room Miss Horaki, how would you like a position that demands respect and will test your skills as a leader?" he asked her, knowing that respect was one of the few things that Hikari had always wanted, and had commented several times that she would give anything to get it. "Suzahara will also be your second in command" he added, knowing her affections towards the jock. It was sealed then, as Hikari agreed to the job.

"Of course you will need to go through proper training first." With that he dismissed the two, having two of the guards take them to the training area. Shinji then turned to Rei. "That went well, now time to deal with Seele" Rei only smiled at this, knowing what he meant. The two then walked towards a separate door that led to the comities hologram meeting room where the six were already present, awaiting the arrival of the Commander of Nerv, assuming it was still Ikari; they were only half right.

"Who are you? Where is Commander Ikari?" the monolith that bore the words SOUND ONLY 01 demanded.

"I am Commander Ikari, my father was forced to retire his command due to health conditions" Shinji explained casually as he sat down at the end of the table, a white light emitting from below him making him look more intimidating then even his father could have succeeded in doing,

"What condition would that be?" another monolith asked.

"The condition that he is dead."

"Why were we not informed of this?"

"Who will finish out plans now that Gendo is dead?" monolith 03 asked.

"I will." Shinji stated "I am well aware of the scenario my father had planned out according to the wishes of Seele. I have viewed over the files and have also seen many flaws in its design." he continued.

"What flaws?" the voice of 01 asked.

"Third Impact will not progress the human evolution, in fact it will end it." he explained. "Evolution itself takes millions of years to accomplish, not decades. However humans adapt by evolving technology to progress through their lives. I just happen to have acquired some technology that will push us as a race even further."

The six contemplated this, evidently the young man had done his homework considerably, and silently agreed at the flaw that he had pointed out. Rei had stood silently beside Shinji as they discussed the possible out comes.

"Very well Ikari, send us this technology so that we may view it ourselves." the monolith 01 said.

"Of course, but I would like to invite everyone to come here to view it, such technology is too valuable to risk being stolen during transportation." Shinji pointed out, one thing that he had learned from Sidious was how playing the political game could win trust over many, making the take over go much smoother.

"Your point is seen, however you will provide the transportation. We will meet in one week" with that the rest agreed and five of them faded, leaving only the monolith 01 there. "In request of the previous commander we have already sent the fifth child, he should arrive there shortly; do not disappoint us Ikari." it said before fading away.

Shinji stood up and grinned at Rei. "Seems we will be having more guests." he stated as the two of them walked back out into his office. Akagi was waiting near the desk.

"Sir, we have finished analyzing the weapon, and can start replicating it with in a week, However we can not replicate its unlimited energy source, so we have created a battery like cartridge to supply power to the laser." she explained. "We can also control the color of the beam depending on what gem we use, ruby making it red, sapphire to make it blue and so on. Do we have your permission to continue sir?"

"Yes, feel free to order as many rubies as you see fit, once you have finished building the new weapons begin to train the personal how to use them, I feel we will need as many as we can get in the future." he said, then dismissed Akagi, he then turned to Rei. "The fifth child is here, why don't you go greet him. If he offers any resistance, you know what to do." Shinji grinned before leaving the room. Rei nodded and left the room with him but split off in a different direction. Stretching out with the Force to see where the fifth child was. She then proceeded to make her way across the base, many of the personal moving to the side as she strode through the corridors. It did not take her long to find the white haired boy.

"You must be the First Child." the boy greeted her, "Though you look far too grown to be an Eva pilot" Rei did not reply to his words, instead she scowled at him, immediately taking a disliking to him. His life would have been spared if he would have ended his words there, he was not so fortunate. "You and I are the same, we should be friends" he commented with a smile. At this Rei halted, her brow furrowing into a scowl. Many of those nearby quickly moved away, having seen that look on her face before. In a sudden movement she took her saber from her belt, ignited the back end of it and thrust it backwards, impaling the boy just below his sternum, completely missing any vital organ, so as not to kill him right away. Smirking she turned and faced him, still holding onto the saber as she twisted it.

"We are nothing alike" she growled at the wide eyed boy, she then thrust the saber upwards, splitting him up the middle from the sternum. Extinguishing the blade she watched as he split, almost looking like a flower opening up. Turning as the body fell she looked at one of those nearby, causing them to flinch under her stare.

"Have someone clean this up" she ordered and left.

Central Dogma

Misato crouched down next to Kaji who was busy hacking his way into various files that the MAGI held. Most pertained to the Human Instrumentality Project, but that wasn't what Kaji was looking for. He had a new interest, the Third Child. Finding a file that contained the rooster of the personal he opened it.

"Well, looks like he has hired three new people, and Asuka was promoted to Lieutenant." he commented.

"What? How did she get promoted?"

"Seems she has sworn her loyalty to the new commander, and has been carrying out his orders."

Misato sighed in despair, deep down she was hoping that she could have talked Asuka into joining her and Kaji into a resistance against the new Commander. Misato didn't like the way things were looking, she had come to terms that the Shinji and Rei she once knew were gone. "Who are the three he brought onboard?"

Kaji didn't answer for a second. "Toji Suzahara, Kensuke Aida, and Hikari Horaki"

Misatos eyes widened for a moment before asking. "What positions?"

"Aida was put with the MAGI team for tech support on the computers, Horaki is now head of Section 2, and Suzahara was placed right beneath her, they are currently under going rigorous training for the positions."

"Putting a child in charge of a security team, have we really gone that low?" she commented to herself.

"Evidently there is more to her then meets the eye, she has already adapted to her new role very well, and has already tightened up some of the security at the exits." He then continued to scroll through a few other files before he came across one that caught his attention. Opening it up he almost fell back in surprise.

Misato saw his reaction and asked "What is it?"

After collection his thoughts he replied. "Seele is coming here, next week"

"What for?"

Before Kaji had a chance to answer they heard the click of a gun being cocked as a light shined on the two. The two could only make out the outline of a long haired female figure standing ten feet away from them, holding a flashlight in one hand and a hand gun in the other, a 9mm by the looks of it. "You know its not a good idea to going digging behind our commanders back." she replied, the two immediately recognized her voice. "It can have serious repercussions." she continued, her voice becoming cold as she leveled the gun to Kaji, without hesitating she pulled the trigger twice, hitting the man once in the chest and once in the head, killing him instantly.

"ASUKA!" Misato cried out jumping up to run towards the girl, only to have the gun pointed at her.

"I wouldn't suggest trying anything." the german girl replied, her voice still cold.

"But why?" tears ran down the womans face as she looked down at her dead lover. "Why did you kill him, I thought you loved him!"

Asuka only shrugged, her aim still on the woman she began to put more pressure on the trigger, before a voice came from the shadows.

"Hold your fire Captain Soryu." the voice said. Misato looked towards it direction to see the shady outlines of three individuals at the end of the corridor, she could make out Akagis lab coat, standing closely near another female, no doubt Rei. She then looked to the middle form who was approaching her his hands held behind his back; it was Shinji. "You plan to betray me" he said flatly, it wasn't a question.

"I.. I-I was jus-" she never got to finish as she began to choke, Shinji had raised up his two fingers pointing at her.

"Those who will betray must be punished, and the punishment is death." he growled the last few words. Slowly choking the life out of her as she began to levitate in the air. Suddenly he released her, letting her drop to the floor. "But because I still have fond memories of you taking care of me, I will not kill you." he said as he turned and walked away, nodding to Asuka as he passed her. Misato was about to stand up when she felt the cold metal against the side of her head, she looked up to see the cold eyes of Asuka before she pulled the trigger. "We have no room for traitors in our midst" Asuka stated coldly as she pulled the trigger. She then turned and walked away from the two dead bodies holstering her weapon, following the other three. Shinji grinned, the Second Childs loyalty was set. He then turned his attention to Akagi.

"You said you had something to show us?" he asked.

Ritsuko didn't answer right away as she looked over at the bodies of the two _'Why couldn't you two just accept the new management'_ she mentally asked herself, then turned her attention back to the commander. "Yes, this way please" she said and lead the small group to the end of the corridor, to a set of large doors. She swiped her card and allowed them access into a small chamber surrounded by an aquarium. Pressing a button on the small remote she held in her pocket, the aquarium lit up, exposing dozens of Reis.

"MEIN GOTT!" Asuka exclaimed as she looked over at the Rei who stood beside her, her face showed nothing of surprise nor disgust, instead a slight smile came across her face. Shinji however sneered at this, seeing so many of his wife.

"Destroy them all" he ordered Akagi. The doctor hesitated for a moment before placing her thumb over the abort button.

"Wait." Rei stated then turned to Shinji. "Master no doubt these would have my same abilities, with training we could make a special task force. We may need such a task force later on." she explained, Shinji nodded, she did have a valid point.

"Very well, we will train them, but only in saber combat" he said then turned to the doctor. "Reanimate them as soon as possible" he ordered.

"Yes sir" Akagi replied. The four then turned and left the room, no one second looking the two dead bodies as they made their way to the elevators taking them back to the top level. Shinji then sent Asuka to go get a more adequate uniform for her new position. Akagi took her leave and went back to her lab, continuing to rebuild many of the blasters she had started, most only missing the ruby to merely color the beam. Shinji and Rei retired back to their room, just above their office. The passed the area that the fifth child was killed in, but there were no indications he was even there once.

"I take it the fifth child resisted?" Shinji smirked.

"He upset me" Rei simply stated as they entered the small apartment like room, it looked much like the ones that were on Coruscant, being elegant yet simple.

Standing in front of the large window that over looked the Geofront, the light beginning to fade as dusk crept over the complex. Below they could see many of the guards training, in front of the rows of training guards was a brown haired girl, barking out orders, or yelling at some who were not in time with the rest. Shinji had already read the report, it did well to have put the young girl in such a position, she had aced the firm arms training and even the tactical combat simulator, showing she had a knack for combat. Beside her was the jock, leading the physical exercises, it was to be expected which was exactly why Shinji had placed him there. True to his word Shinji had the young boys sister transferred into Nervs hospital with in the hour after the boy accepted the position. Rei stood beside him, looking over the scene with him, one hand down at her side while her other held her belly.

To Be Continued……

Authors Notes: Wow, Rei has got one vicious streak in her! Course not knowing how to vent your anger and keeping it inside for nearly 14 years, you'd be a little short fused too. Shinji has been taking a more political approach, but don't worry; his dark side will show soon enough. And the real shocker, Asuka kills both Kaji AND Misato. Well Misato is actually understandable, can you imagine trying to live in the same apartment as the woman whose lover you just killed in front of her? I am surprised though that no one has said anything about Fuyutski getting killed off. As requested I threw in Hikari, Toji and Kensuke into this little dark force. I was originally place Hikari as a secretary but decided against it feeling it would be best to place her with Toji as she is fond of the dumb jock.

Who is Master C'baoth? He's actually a dark Jedi from the Timothy Zahn Star Wars books. I thought he would be a great err good guy? Bad guy? I will be going into more detail about the Chikara crew in the third and final installment. Hope everyone enjoyed this update.

Pre-Readers

Gunman

Sarina Voegeli

Disclaimer: Neon Genesis Evangelion and characters are property of Gainax and all other respective owners. Star Wars in property of George Lucus. Master C'baoth is property of Timothy Zahn and respected publishers.


	3. Episode 3

Dark Child the Return

Episode 3: Rise of the Sith

By Midnight Lost

Original Concept by Gunman

I apologize for the delay in updating this, I took a small break to try and get passed my writers block, during that time I got distracted with World of Warcraft, thanks for the sympathy lol. Anyways, this chapter was more difficult as I have two large fights both going on at the same time, and I hope you wont be disappointed. Yes, I have made Rei a little too savage, I guess that because I was trying to show how much becoming a Sith has altered her, however in this chapter I will be focusing more on the darker side of Shinji, poor Seele wont know what hit them. Just so everyone knows there are some small time skips in this chapter. Also you may notice my pen name has changed, this is still shinjitheassasin, I have just embraced a pen name that more suites my personality. Alternate ending as well D

**MAGI Room**

Asuka strode in to the Magi room, picking up reports to review. It had been just under a week since Katsuragi's termination, Asuka was promoted to Major, and was also put in charge of her duties. She did feel a slight twinge more respect for the former major for everything she had to put up with but the job wasn't too hard. When she entered the room, she gained many curious stares. The others didn't know about Misato yet.

"Where's Misato?" Hyuga asked, pushing his glasses up on his nose.

"The commander suggested she go on vacation." Asuka stated coolly as she collected the clipboard from Hyuga regarding the tactical data of a presumed attack against the base. Shinji had already voiced his concerns on the matter and had ordered the MAGI team to formulate a defense that could hold a large force at bay for sometime. To do this, they began to cut any outside lines they had, making the base itself self supporting. This was done without Seele's approval. The three bridge bunnies didn't like the idea of it but followed the orders.

"She never said anything about it" he commented.

"She seemed to be having a hard time with the change of leadership." Asuka stated, becoming rather annoyed with the direction this line of questions were going. "So the commander ordered her to take her vacation"

"What about Kaji? Haven't seen him around lately, though I think a few of the females her are thankful for that." he snuck in a little joke, causing some of the female personal around him to blush at the memories of the unshaven man forcefully flirting with them.

"Kaji was caught conspiring against the commander, and was dealt with accordingly." Asuka stated coldly

'_So, I guess he did get caught, probably executed on the spot knowing the new commander.' _Hyuga thought, remembering nearly a week ago when Kaji had approached him about joining a resistance movement against the commander, Hyuga had declined, not wanting to get himself into anything that could cost him his life. _'Glad I didn't join him, or I would be dead next to him'_

"Well, congratz on the new promotion." He said as he handed Asuka the final clipboard.

"Thank you" Asuka smiled then turned and left the room.

**Commanders Office**

"How is the clone training coming along?" Shinji asked his blue haired wife.

"It is complete, they are sufficient enough to hold a small task force at bay." she informed him. A week ago he had already told her, and the defensive troops of a strong attack from a task force with the same technology. At that time, Rei focused on training her clones in light sabers, for security reasons the two Sith did not teach them anything of manipulating the Force. In turn, Hikari had increased the security surrounding the base.

"Very good. I am sure the Jedi will be in for a surprise." Shinji laughed, adding venom to the word Jedi.

"So today, the committee is visiting?"

"That is correct. You will be accompanying me during the meeting." he smiled, Rei returned his smile.

The two were interrupted when a there was a knock at the door.

"Enter." Shinji spoke. At those words, Hikari entered the room, dressed in a standard Nerv uniform, bars on her chest to show her rank as head of Section 2."Report"

"Sir, motion detectors north detected a large group of humanoid beings moving slowing in this direction. They have seemed to stop, roughly a mile outside the city to set up camp. No more movement in this direction has been detected in twelve hours."

"I see, they will attack at night, possibly hoping security will be lighter during the nightfall to put up less resistance." he concluded.

"Also, the transports carrying the committee members have begun to arrive Sir." Hikari finished.

"I see, ensure that all soldiers are at their stations. We don't want to give them the false impression of how this base is ran." he smiled. Hikari knew very well what he meant, he wanted the committee to feel a false sense of security, and she was to play a part in it. She didn't like the idea, but after being informed of the committee's background, as far as Nerv knew, she felt this was the best course of action. Without the committee the UN would not be able to initiate an attack against the base, at least not a full fledged attack.

"Yes sir." with that, Hikari left to carry out her duties.

"Shall we go and greet our special guests?" Shinji laughed. The two then left the large room towards the meeting room where the committee was already beginning to gather at. It was a few minutes before Shinji and Rei reached the meeting room, it was a rather large room with a long metal table in its center. There were three doors leading out of the room, in a triangular form. Once the two entered the large room, they were immediately bombarded by questions from Kael.

"What is she doing here and where is Fuyutsuki?"

"I am sure you gentleman know Rei Ayanami, as for Fuyitsuki, he is currently in the medical wing recovering from a heart attack." Shinji began.

"We are well aware of who she is, but that does not explain why she is present here, this meeting does not concern the Eva pilots."

"Ayanami is no longer an Eva pilot, she is my second in command." Shinji answered as Rei stood silent behind him, shrouded in her black cloak,

"Very well, I suppose we shall bring this meeting underway." Kael announced. "Before we discuss this new technology you possess, we are curious as to why the Angels seemed to have cease their attacks."

"Yes I thought you would inquire about that, and I have an answer as well. You see, when the previous commander died, we discovered he had Adam, grafted to his hand, much like a parasite. However when he died, Adam had nothing to live on and perished as well. My only conclusion is that the Angels no longer have a goal to achieve they have retreated back to where ever they come from."

"So, it would appear Gendo planned to betray us." one of the committee members mused.

"Very well. It would appear our original plans would have failed regardless. Now bring forth this technology so that we may view it with our own eyes."

Shinji nodded, a small evil smirk coming across his face, which made the others in the room feel uneasy, except for Rei. Stretching out with one hand he pointed to one of the doors on the side of the room, motion two fingers down, the door began to close. He then repeated the same action to the remaining door, leaving no exits open.

"What is the meaning of this Ikari?" Kael demanded.

"Not only will I show you this new technology. I shall let you feel its power." Shinji laughed.

"Shall I do this one Master?" Rei offered.

"No, I think I will take care of this." Shinji commented, bring out his right hand to his side. As soon as he did so, a cylinder object shot from the side of his hip into his hand. He then ignited his light saber, its red glow lighting up his face, casting a air of doom on the committee.

"What is going on Ikari?" Kael demanded again. Shinji gave him his answer through actions. Leaping with inhuman speed, he landed on the table, quickly slicing to his right. Seconds later the thin mans head rolled off, landing on the ground. Looking to Kael, he throw his free hand out towards him, sending blue bolts of lightning at him. Knocking the older man out of the chair and into the wall. Smoke rising from the mans weary body. Shinji then turned his attention back towards the others, thrusting the saber into the throat of fat Texan, then brining the saber up to cut the head in half from the throat up; allowing it to bloom. By this time the remaining two had already jumped out of the seats, desperately running towards one of the exits. Unfortunately they both ran to the same exit. Again with inhuman speed, Shinji cut them off, igniting his second light saber doing a spin in mid air as he bound over the two, the saber blades slicing each of the men in two places. One at the neck and the other at the waist, before the young Sith landed in a crouched position as the parts of the two bodies fell to the ground. By this time Kael had regained his senses, shaking the cob webs from his head he jumped to his feet and ran to the door nearest to him. Opening it, he dashed out, running down the hall way. Shinji looked on and smiled.

"Will you not go after him Master?" Rei asked.

"No, there is someone already waiting for him." he answered.

Sure enough, as Kael rushed down the halls he ran into a brown haired girl, dressed in a black Nerv uniform,

"THE COMMANDER IS TRYING TO KILL ME!" Kael exclaimed.

"I know." Hikari stated, raising her hand, exposing the black barrel of her side arm. She leveled the gun to the mans head, and pulled the trigger without hesitation. A lone tear had dropped from her eye as she did so, she had lost her innocence. She holstered her weapon and turned, facing the Commander as he walked up to her.

"Well done" Shinji commended her.

"Just following orders sir." Hikari said. Her voice shaking a little, still a little shocked by what she had just done. Her eyes shifting to the floor.

"You executed your orders with satisfaction Captain." Rei commented.

"Thank you" Hikari smiled at the sound of her new promotion. She couldn't help but think that now she was getting the respect she had always wanted, but at what price.

"See to it that your men clean up this mess Captain." Shinji ordered, securing his sabers back to his belt.

"Yes sir." Hikari stated and walked away to do so, stepping over the corpse of Kael without a second look. What's done is done, there is no turning back now, only thing she could do is move forward, however this is one event she knew she could not talk to her younger sisters about. Every night after her shift her sisters would always ask what she did that day, and how it is like working at Nerv and under the command of the new Commander.

After Hikari had left, Shinji then turned to Rei. "Our plan is nearly complete. Now with Seele out of our way and the U.N. forces under our control there will be nothing to stop us."

"Who will you leave in charge of the U.N.?" Rei inquired; curious as to whom he would trust with such a force.

"The very person who had just executed the head of the committee." he replied as the two began walking back towards the Command room.

"I see."

**Akagi's Lab**

"DAMN IT" the blonde haired woman spat as another spark came from the wirings of the blaster she was trying to put back together. It was the same blaster that Shinji had given to her to replicate. She had succeeded in replicating it to the best of their technology; building enough of the new weapons to supply a small defense force. She had already issued the weapons to Hikari; instructing her how to use them so that she may teach her own troops.

"Are you alright Sempai?" Maya asked as she approached the blonde woman.

"I'm fine. How is the painting coming?"

"We've concluded we have enough of the paint to cover about 67 of all the walls in the base with it, however during tests the paint will only hold up to five shots in one area."

"I see, focus on the main routes. If the commander is right about this task force that is to attack, they will not be familiar with the layout and will opt for the main hall ways.

"Yes ma'am" With that, Maya left to relay the orders to the maintenance division who was in charge of the painting.

Ritsuko then turned back to finish putting the blaster back together, only to receive another shock from a loose wire.

"GOD DAMN IT!"

**Chikara Base Camp**

It had been just over a week since his ship had crashed into the ocean. His apprentice gone and his own troops now beginning to lose their moral. Though none could be certain as to why, they all knew they were never returning to their home. The elder Jedi once again found a small hill over looking the encampment. Many of the troops were looking over their weapons ensuring that they did not take no damage and that it would not fail them during their siege on the base. The entire platoon was unaware that they were being tracked, but C'baoth knew.

"Gentlemen" he called out from atop the hill, getting the attention of those below him. "Our enemy knows we are coming. Our plan to attack the base at night will not hold the element of surprise as you have hoped for."

"Then what do we do sir?" a lone soldier asked.

"We proceed as planned." the old man smiled

"But sir, you just said the attack would fail."

"I said no such thing of failure, I said we no longer have the element of surprise." the jedi countered.

"Then how do we succeed in this attack? The bases defenses out number and outgun us" another pointed out.

"Your attack will divert the defenses attention and draw them away from the base, while I infiltrate. Once I dispatch of the Sith, the base will then be under my control."

"Understood sir." the Lieutenant spoke finally. He then turned to the troops behind him as the old jedi faced away from them, looking towards the base. "You heard him, prepare to attack, we move in six hours!" the younger man ordered.

**Six Hours Remaining**

Hikari entered the commanders office after being summoned there. She wasn't told why she was called, only that the commander had a new job for her.

"Sir, you wished to see me?"

"Yes Captain. I have a new assignment for you and Sergeant Suzuhara."

"Sir?" Hikari asked, a little confused.

"With the Committee no longer pulling the strings on the UN Forces, someone needs to assert their authority over them. You have proven yourself capable of handling such a task; despite your age." Shinji began to explain to her, sitting behind the large desk with Rei standing at his side, her hand on his shoulder.

"I understand, but why Suzuhara as well?"

"You two work well together, and do you not hold some feelings towards him?" Shinji ventured. At these words Hikari blushed uncontrollably.

"No…I mean… that …is I…" the young captain stumbled over her words. This caused Shinji to laugh a little. The first good natured laugh he has had since his training. Rei also let out a small chuckle.

"Relax Captain; I may be harsh, but I am not blind" Shinji said as he stood up, making his way over to Hikari. "So; do you accept the assignment?"

A glint of determination shined into Hikaris eyes as she snapped to attention "Yes sir."

"Good." Shinji patted her on the shoulder. "I will leave it to you to inform Suzuhara. I suggest that is not the only thing you tell him." Again Hikari blushed, knowing full well what he was implying. After she had left Shinji then turned to Rei.

"Let us go visit our ward in the medical wing." Rei simply nodded in reply. With that the two began to make their way down the series of corridors until the reached the medical wing. Reaching one of the many doors, Shinji pushed it open to reveal and elderly man laying in one of the beds. His short grey hair went every which way as it had not been combed for some time. Stubble lined his thing face. Slowly the man opened his eyes, blinking them a few times. He didn't recognize the man that stood there, but as soon as his eyes lay rest on Rei they shot open in horror; memories flooding back into his mind when she had mercilessly killed the commander before him. His heart monitor beginning to beep more rapidly, threatening to bring on another heart attack before Shinji used his influence of the Force to calm him down.

"Evening Fuyutsuki, how are you recovering?" Shinji asked.

Fuyutsuki blinked again a few times. "Shinji? Is that you?" he asked, somewhat sounding like he unsure. His eyes darting back and forth from the young commander and the blue haired girl next to him.

"Yes, though I am now Commander Ikari" he informed the old man. "Do not worry, if Ayanami wanted to kill you she wouldn't have had you brought here after your heart attack.."

Fuyutsuki nodded at the words of assurance. "I apologize for my actions earlier, the last thing I remember is a flash of red, and then Gendo was dead."

"Yes, my father had to be removed from command." Shinji stated.

"What about me?" Fuyutsuki asked, afraid of the possible answer.

"You? Weather you decide to continue to serve Nerv or not is up to you."

"I see."

"However, be assured that if you stay with us, the rewards shall be great. Perhaps you would like to be reunited with an old colleague of yours." Shinji smiled

"W-what?"

"Unfortunately if you do stay with us, you will no longer be the Sub-Commander, that position has been given to Ayanami. She does such a wonderful job." Shinji smiled. Fuyutsuki only nodded, not daring to object to anything to young sith said. He had witnessed first hand of Reis savagery when she attacked the previous commander, and if young Ikari was her master he did not wish to see what he was capable of.

"I understand."

"So, what is your decision?" Ayanami finally spoke. This snapped the elderly man out of his thought process.

"I… I will continue to work with Nerv." Fuyutsuki agreed after much thought. "What does the committee know of Gendos death?"

"Seele is no more. I liquidated them earlier today" the young sith grinned. "So now the entire U.N. is under our command."

"WHAT!?" Fuyitsuki asked in surprise.

"It's simple. We lured them here as a trap and dispatched them immediately' Rei smiled.

"Rei; we should evacuate this wing before the attack begins." Shinji suggested.

"Yes Master." Rei replied and left the room to give the orders to the nurses in the medical wing.

"Attack? What attack?"

"Nothing you should be concerned with. You are in no condition to aid the base so you will be evacuated along with the rest." Shinji said. "Now, if you will excuse me I have other matters I must deal with." After saying that the young commander turned and left the room, quickly accompanied by Ayanami, leaving the elderly man with his thoughts.

**Five Hours Remaining**

After visiting with Fuyutsuki the two then made their way towards the experimental wing, where Ritsukos lab was. By now she had finally finished rebuilding the original blaster when the two walked in.

"Yes Commander?" the blonde haired woman asked as she twisted in her chair to greet the two. With the exception of a few details, she didn't mind the new leadership over the base. Things had progressed much faster under their control then Gendo would have ever thought imaginable.

"I have come to check up on our little experiment." Shinji informed her.

"Yes; of course. The blasters have been finished and were given to Captain Horaki to train her troops." Ritsuko informed them as she stood up; motioning them to follow her to where the real experiment the commander had asked about was. This experiment was under classification, no one other than herself and the two sith knew of its existence. She led them into a small elevator that took them down to the laboratory in Central Dogma. Rei was quiet familiar with this place, it had been where she was born and where she had recently trained her clones to use their own light sabers.

"Both are forming nicely with in acceptable perimeters. However we have had to make altercations to this one." The doctor said as she gestured to one of the tubes that held a human figure of a woman. "We had to graft on the scare. As for the eyes, that's a different story."

"What about her memory?"

"Everything up to the incident has been restored, she will wake thinking she suffered a concussion and was in a coma"

"Very good." Shinji replied.

"Have you spoke with Fuyutsuki yet regarding his service?"

"Yes, we talked with him before coming here. He has agreed to stay on." 

"So he knows who will be waiting for him?"

"No, I made no mention as to who it was he would be reunited with."

"I see. Well, these two should be ready by the end of the day. They are just undergoing final tests to make sure everything is perfect; so to speak." she added, knowing there was no such thing as perfect in science.

"Good. Dr. Akagi. It would do you well to prepare yourself. I believe the attack is coming tonight." Shinji warned her. Since his first arrival back at Nerv he has come to appreciate the doctors abilities as a scientist and didn't want to lose them yet.

"Understood. Should I activate the sentry system?" she asked, referring to an automatic defense system that was put in place some months back to defend against a possible invasion.

"That wont be necessary. I believe the attack itself will be a diversion, knowing how my enemy thinks. The likely target will be myself more then likely.. We will just have our defenses push back the enemy then send out Unit 02 to finish up the enemy.

**Chikara Encampment Three Hours Remaining**

"SIR! Scouts have reported many vehicles leaving the base." a spry young ensign reported to the jedi who still sat about his small hill

"Probably evacuating all non combat personal. Our enemy is not stupid." the jedI spoke.

"What are your orders?"

"Leave them. I have no intention of leading a massacre of non combatants. We shall stick with the original plan."

"Yes sir." with that the ensign left to attend to his other duties.

'_They already know we are coming, and are preparing. But how? Is his knowledge of the Force that powerful or….'_ The jedI stopped his thought process when he noticed a small glint from the corner of his eye. Following his eyes to it he saw it. A small wireless camera in a tree. Hidden under a bunch of leaves. The old jedI couldn't help but smile at it. He then began to notice other things, a motion detector disguised as a mushroom and a microphone that looked like a stick. _'Of course. Our equipment wouldn't detect such a low technology.'_

**Nerv, HQ Thirty Minutes Remaining**

Unsure when the actual attack was going to take place, Shinji had Hikari step up security to its highest status for twenty-four hours. He knew the attack would come before that time was up, it was just a matter of when. The young commander contemplated these things as he stared out the large window from his office, over looking the Geofront. He remembered back when he first saw it, how beautiful it was, surprisingly despite all the battles it still held that same vision. The blue haired sith next to him looked over to him as she took his hand into her own.

"We will be victorious by dawn." she spoke to him softly.

"It is not us I am worried about."

Rei only looked at him questionably .

"I worry for those inside the base who will possibly die in this attack." he told her. He knew it didn't sound sith at all. Truth was, he was slowly losing his hate and turning closer back to the light. Rei, of course was following him, but for other reasons as well.

"We shall just have to protect them as well." Rei offered. Shinji only smiled at her comment and gently squeezed her hand.

The two were interrupted again when there was a knock at the door.

"Enter" Shinji called as he turned to face the person entering through the doors.

"Sir. Defenses are in place." Hikari reported.

"What of the UN Forces?"

"They were shocked at the news of the assassination of the committee and offered to send reinforcements to aid us against the attack."

"Make it so. They are already on the move as it is. Also, I want you to pull back the outer defenses. Allow the enemy to enter the Geofront. Once they are inside bring about a small force from the rear to trap them in a cross fire." Shinji said as he glanced at one of the screens that was on his desk, showing a large troop moving towards the base.

"Yes sir." Hikari said and left to call in the reinforcements, though she doubted they would really need any. The attacking troop only number around thirty six. But then again, she was realizing how the young commander thought. This request no doubt was to gain the support of the UN. The young Sith then turned to his wife.

"We should prepare ourselves. Locate your students in the side hall that leads directly to this room."

"Yes master." Rei said and left to do so. Shinji took one more glance outside the window before sitting back down in his chair behind the desk. He knew the jedi would come for him, partially the reason he wanted to get Rei out of the room , so she could not be used against him.

**The Attack**

Just as the young Sith had predicted, the outer security doors were blasted open before the time frame was up. Immediately the base went on Red Alert. Defense groups all around the base scrambling with their weapons to cut off the intruders. Both sides met in the main hall and quickly faced off. Each side taking what ever cover the could to avoid the blaster shots. However, Nerv had the advantage as they took shelter behind the protective paint wall, and was able to fire through the other walls. Quickly the enemy troops began to fall. The jedi saw this as a loss cause and ordered his troops to pull back as he quickly darted into another corridor, only to be met by thirteen blue haired Sith. The leader of this squad standing much taller then the others.

"This is as far as you go jedI." Rei spat.

The old jedI only chuckled some. "It seems you two have become well prepared. However, it is not you who I am after." He raised his hand up pointing his fingers towards the clones; closing his eyes for a moment, then opening them slowly, a smile still plastered on his face. "Now, I shall leave you to play with your selves." the old man laughed as each of the twelve clones ignited the sabers and turned towards Rei. In response Rei ignited her own, having a strong indication what had just happened. She then ignited the other side of her saber so that now both sides held a red blade.

"Try not to kill yourself" the Jedi laughed and jumped over the group and continued on his way. He had no time dealing with an apprentice, he was here for the Sith Lord himself.

Rei sneered as the jedi ran off, but she had faith in her husband to kill him. Turning her attention back to her clones. She didn't have to wait long as one rushed at her, its saber quickly being deflected then being impaled in the heart. After killing the first one Rei looked over the remaining who had watched. No doubt the first was to test the siths speed in battle.. Three more rushed her, putting her on the defensive for a moment as she fought to block and deflect the on coming slashes. In another split second she ducked out of the way of one of the slashes, once down in the crouched position she didn't give her opponents anytime as she twirled her double edged saber over her head, cutting them in half at the waste. Before she was even standing two more had rushed her, but she was prepared as she came up, spinning on her heels she used her own neck to rotate her saber. Its blades narrowly missing her own neck as it cut through the necks of the others. Catching her saber she looked at the remaining six, a grin on her face. This was the exact reason they were denied any training in the force.

"Now then, let us stop playing around. It is obvious the only chance you have against me is to attack as one." Rei smirked as she twisted the handle of her saber into two opposite directions, splitting the saber into two different blades. She then twirled them in her palms so she was holding them correctly. She didn't give them time to respond as she went on the offensive. Two of them didn't have time to even block as she jumped up, and spun around, taking off the heads before she even landed in the center of the remaining four. She then spun around again, a flurry of blades striking everywhere as the remaining four fought back. Sparks flew as the blades cut into the walls and ceiling, shutting out the lights. Only the red glow of the sabers lit up the corridor, giving it an eerie appearance. Rei throw out two fingers towards one of the clones, sending it flying back into the wall, breaking its spinal column when it impacted against the wall. The other three jumped back away from the sith to try and put some distance between them, but it didn't work. Rei rushed in again, block two of the sabers she then turned again freeing one of her sabers to block the third. While the first was distracted she took the opportunity to thrust her second saber into its chest, pulling it out again just in time to block another attack. Again the remaining two jumped back, this time Rei did not follow. Standing where she had killed the other clone, she dared them to attack her, watching them both. However one of them caused her to worry a little. Through out this fight she had noticed it was purposely staying back, purposely sacrificing the others. Rei knew that it was learning from the others mistakes and was formulating ideas to correct each mistake the others had made. She didn't have to wait long as the first of the remaining two attacked, wildly swinging its saber in every direction, being rather unpredictable in determining where the blade was going to fall. Much like a wild beast. That was when it happened. Foolishly Rei had focused on the attacking clone that she didn't realize the other had gotten behind her. After the wild clone made a futile swing, Rei moved in for the kill, thrusting her own saber into the throat of the wild clone. As she did so however she felt a sharp, burning pain in her left shoulder as a saber went through it, forcing her to drop her left handed saber.

"You should never take your eyes off your opponent, sensei" the clone hissed into Reis ear as she pulled the saber out of Reis shoulder. Once free Rei turned to face the clone. Now she was at a disadvantage with the use of only one arm. Her other saber still in the throat of the dead clone. The wound in her shoulder would take far too long to heal, even with her Angel abilities.

"After I've killed you I can take your place by Shinjis side." the clone smirked. That's when Rei realized, this one wasn't under the control of the jedI at all, she was acting on her own will, it all came together in that second why this one had purposely sacrificed the others, not merely to just learn Reis moves but also to eliminate any other competitors.

"And what makes you think he will accept you clone?" Rei spat, the thought of this woman taking her place aggravating her to say the least.

"I am not just a mere clone of you, I am Lilith" she smirked "And I can offer him things you are unable to."

"And what would that be?"

"I can give him the world, without hesitation or conflict. After all the entire human race are my children, and I can control them." Lilith said "And, I can offer him my virginity again. Men love taking that from a woman. The feeling of exploring a new virgin territory." Lilith continued.

Rei couldn't help but laugh.

"What do you find funny?" Lilith questioned.

"You truly do not understand Shinji. He will not act on lust nor will he accept the world you offer him."

Lilith looked at her questionably . What she said didn't make sense to her. Isn't that what all men want and crave. Lust, sex, power and control?

"If your going to do something you shouldn't just talk about it." A female voice called out followed by a blaster shot. The laser hit Lilith in the forehead, the coil of the blast knocking her head back. Rei knew that wouldn't be enough to kill her and quickly took her saber out of the dead clone and thrust it into the abdomen of Lilith, piercing the S2 engine. As she did so, Lilith began to implode upon herself until there was nothing left. Rei then turned to look to the new arrival and saw a lavender haired woman in a red coat standing at the end of the hall with a blaster in one hand. The woman quickly holstered her weapon and quickly walked over to Rei.

"I apologize for being late." the woman said.

"Thank you major." Rei said, looking up into the crimson eyes of Misato.

**Commanders Office**

It only took the jedi a moment to get to the large wooden doors. He could feel the sith waiting behind them. Using the force he pushed them open to see the young sith lord sitting behind his task, his hands folded in front of his face, sitting much like his father would have. Once the jedi fully entered the room, Shinji motioned two fingers towards the doors, sealing them shut so that no others could come in to interrupt the fight that would start soon.

"I was beginning to worry you would not make it." Shinji broke the silence.

"I apologize for making you wait then." the jedi laughed. There was a small beep from the commanders desk. Shinji pushed a small button the answer the call.

"Yes?" he asked, still not taking his eyes off the old man.

"Sir, the enemy has been pushed back into the Geofront and are retreating into woods." came a females voice.

"Thank you Captain, pull your forces back and send Asuka out in Unit 02 to finish up the clean up. I am sure she would enjoy that."

He then turned his attention back to the Jedi. "Please, join me at the window. And watch as your pathetic task force gets wiped away." Shinji said as he got up from his desk and walked over to the window. Though he now had his back turned to the jedI he never dropped his guard. But the jedi accepted his offer, taking a spot a few windows away. Below the could see laser blasts flying back and forth, red and green and blue. C'baoth was about to say something when a flash of lights just below him began flashing, alerting others nearby to clear the area.

"What could one unit…" the jedi was cut off when he saw the unit in question. A giant red robot emerged from the ground in front of the window.

"This is Evangelion Unit 02. A highly advanced bio mechanical robot which was used to battle other enemies far stronger then your little task squad." Shinji informed him. "But enough with the pleasantries." the sith said as he removed his robe, leaving him in his standard uniform. The jedi did the same and drew his saber, igniting the blue blade. Shinji did the same, bringing out both of his own sabers, igniting them both

"Shall we begin?" Shinji smirked. He got his answer immediately as the older jedI lashed out with his saber, but Shinji deflected the attack easily and proceeded to put the jedI on the defensive as Shinji spun around attacking with both sabers. The jedi was clearly having a hard time defending the attack of both sabers, but managed to keep up somehow. Jumping back to give himself room to formulate a plan to bring down his foe. As the jedI did this Shinji spoke again.

"What shall I place on your grave? Surely one who has made it this far is worthy of recognition."

"Jorus C'baoth, Jedi Master. And I do not intend to die."

Shinji only smirked "No one ever plans to die. It just happens." At the end of that phrase Shinji twisted his sabers in his hand so that he was holding it blades down and leapt up into the air towards the older man, bring his saber down onto the jedis, briefly knocking it away, with the free saber he slashed at the mans head but missed as the man ducked out of the way, coming up behind Shinji and bring the blue blade down towards him. Shinji however saw this and quickly brought his other saber back, block the attack. Shinji then went back on the offensive turning around, what appeared to have been mad swings were perfectly controlled, causing a brilliant light show each time the red blades hit the blue blade. The old man ducked again swinging at the young siths legs but missed as Shinji did a side flip over the saber, turning around again to face the older man, crossing his own sabers lurched forward and spun one saber so that it stayed on the others blade. Forcing the old man to retreat some before moving back in. Catching the handle as the blade spun, Shinji then turned his back to the man and leaned fully back, the blue blade narrowly missing his head as he slashed the old jedis waist. Coming back around he stuck his sabers into the ground as the old JedI stood there, still in shock what had just happened, before he fell to the ground in two parts.

"You put up a good fight, you will be remembered." Shinji stated as he extinguished his sabers, securing them back to his waist. At this time Rei came in, accompanied by Misato.

"Are you all right Master?" Rei asked, her own wound having already regenerated itself.

"Yes, it is over now." Shinji answered with a sly smile across his face. He then turned to Misato. "Evening Major, please notify everyone that we are no longer under Red Alert." Misato nodded and left to do so.

The two then walked over to the window over looking the Geofront. Below they could see Unit 2 returning to the hanger bay as the U.N. Army finally arrived. Hikari was already reporting to the field commanders of the situation. Everything had gone according to what Shinji had planned.

"So what now Master?" Rei asked as she looked over to her husband.

"Well," Shinji thought for a moment. "First of all, please call me Shinji."

Rei only smiled. "And then?"

"And then," Shinji pulled her closer to him so that she was standing just in front of him, placing his hand on her belly "We look towards the future." he whispered into her ear, causing her to blush a little.

**One Year Later**

It had been one year since Shinji and Rei had returned to this world. Though they had started out with darker ambitions, something had caused them to change the foresights to a more brighter future. That something was what Rei Ayanami now held in her arms as she sat on top of a small hill over looking the Geofront. Much of it had changed over the year. Shinji had opened in to the public so that others could see its beauty. In the lake small boats sailed back and forth in the calm waters. She then turned her attention to her daughter she held in her arms as the child slept peacefully.

"Is she still asleep?" Shinji asked as he came up behind her, quietly sitting down beside her. Both had changed their black attire for more colorful clothing. Rei had adopted a new blue outfit that really brought out her eyes, which Shinji loved. Shinji on the other hand seemed to look much like his younger self, in his usual black slacks and dress shirt. However both continued to carry their sabers, they had just modified their blade colors, Shinji changed his to blue and Rei had changed hers to purple.

"Yes." Rei answered.

"Well, I have to get back to the base." Shinji sighed, it had taken him longer then he had expected to get to the hill "Aida wants to go over the Magi report again. And of course Horaki and Suzuhara are on their Honeymoon."

"I am going to stay here longer, Akane likes it her." Rei smiled as she gestured toward the child in her arms.

"Well, you two behave yourselves" Shinji laughed, his statement causing Rei to giggle as well.

Fifteen minutes later Shinji reached the base. He was greeted by Fuyutsuki as he walked out of the building with a girl hanging on his arm. She was very slender and had short brown hair.

"Afternoon Commander" the elderly man greeted.

"Afternoon General." Shinji replied as he entered the building to take care of the tasks that were required to get done.

Shinji couldn't help but think that despite the road he had chosen and the choices he had made. That things were only going to get better. The angels were no longer a threat, neither was Seele to force the Third Impact. Though he had taken crude actions to see to such out comes, he felt it was required.

End

**Alternate Ending**

"Are you all right Master?" Rei asked, her own wound having already regenerated itself.

"Yes, it is over now." Shinji answered with a sly smile across his face. He then turned to Misato. "Evening Major, please notify everyone that we are no longer under Red Alert." Misato nodded and left to do so.

The two then walked over to the window over looking the Geofront. Below they could see Unit 2 returning to the hanger bay as the U.N. Army finally arrived. Hikari was already reporting to the field commanders of the situation. Everything had gone according to what Shinji had planned.

"So what now Master?" Rei asked as she looked over to her husband.

"Well," Shinji thought for a moment. "First of all, please call me Shinji."

Rei only smiled. "And then?"

"SHINJI YOU IDIOT!" Asuka yelled as she kicked the sleeping boy out of his bed.

"OW! What the hell you do that for." Shinji retorted at the fiery red head.

"Didn't you hear the alarms? Theres an Angel attack and here you are sleeping. Now lets go."

Shinji groaned as he stood up, rubbing the side of his head. _'Shit, it was only a dream.' _He thought. Running out the door to catch up with his fellow pilot who was already half way down the block. He then skidded to a halt when he looked up and saw the zebra stripped sphere floating above the city, suddenly experience a strong sensation of déjà vu.

**Additional Notes**

Well there it is, the conclusion to this trilogy. I had a lot of fun writing it and hoped every one enjoyed reading it. Special thanks to Gunman for allowing me to run with this. Later on I may revise this entire trilogy, adding more detail in certain areas, but for now thanks for reading. Some may think the transition from dark to light happened way to fast, and perhaps they are right; however a change of heart doesnt need to take decades. As for Rei naming her child Akane, Akane was a character I originally introduced in one of my first fics and she has stuck. Most have also come to the conclusion that the woman accompaning Fuyutsuki is Yui Ikari; and you would be right. Ja ne

**Disclaimer**

As everyone knows, Gainax and its respected partners own Evangelion and characters. Star Wars and characters are the creation of George Lucas. Jorus C'baoth is the creation of Timothy Zahn and any other respected owner.


End file.
